- recipe bioconductor-sigspack
Mutational Signature Estimation for Single Samples
Single sample estimation of exposure to mutational signatures. Exposures to known mutational signatures are estimated for single samples, based on quadratic programming algorithms. Bootstrapping the input mutational catalogues provides estimations on the stability of these exposures. The effect of the sequence composition of mutational context can be taken into account by normalising the catalogues.
- package bioconductor-sigspack¶
- depends bioconductor-biobase:
- depends bioconductor-biostrings:
- depends bioconductor-bsgenome:
- depends bioconductor-genomeinfodb:
- depends bioconductor-genomicranges:
- depends bioconductor-rtracklayer:
- depends bioconductor-summarizedexperiment:
- depends bioconductor-variantannotation:
- depends r-base:
- depends r-quadprog:
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-sigspack and update with:: mamba update bioconductor-sigspack
To create a new environment, run:
mamba create --name myenvname bioconductor-sigspack
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).
Alternatively, use the docker container:
docker pull quay.io/biocontainers/bioconductor-sigspack:<tag> (see `bioconductor-sigspack/tags`_ for valid values for ``<tag>``)